Re: [gmx-users] MBAR issue

On Fri, 11 Nov 2016 09:04:35 +0100 gozde ergin wrote: > Dear all, > > I follow James Barnett tutorial of “Methane Free Energy of Solvation” > however I use betaine molecule other than methane. In order to > analyse the data I use alchemical_analysis.py code however I get

Re: [gmx-users] steered molecular dynamics

What exactly are you looking for ? http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Computing_potentials_of_mean_force%3A_Justin_Lemkul,_Session_2A -- Gromacs Users mailing list * Please search the archive at

[gmx-users] MBAR issue

Dear all, I follow James Barnett tutorial of “Methane Free Energy of Solvation” however I use betaine molecule other than methane. In order to analyse the data I use alchemical_analysis.py code however I get an error : pymbar.utils.ParameterError: Warning: Should have \sum_k N_k W_nk = 1.

[gmx-users] steered molecular dynamics

Hi everyone, I would like to run steered molecular dynamics (SMD) in my protein complex system. I have studied the tutorial of umbrella sampling in gromacs. Can anyone suggest me about SMD? Thanks in advance. Best Regards Mouri -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Invalid order for directive molecules

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

Re: [gmx-users] Invalid order for directive molecules

Hi, I'm pretty sure the right way to use the Martini force field is not to embed it in the OPLS/AA force field. Please follow their instructions :-) Otherwise, almost certainly your polymer's itp file does not conform to the right format. Look for examples, e.g. in chapter 5 of the GROMACS

Re: [gmx-users] Hydrophobic interaction analysis

On 11/11/16 03:53, Mijiddorj Batsaikhan wrote: Dear gmx users, I simulated several peptide's folding. I would like to know the effects of hydrophobic interaction for the folding. How can I make analysis and know the effect of hydrophobic interaction? Is it possible to assess the hydrophobic

Re: [gmx-users] [gmx-developers] ecomposition of Lennard-Jones contributions in free energy calculations with Gromacs

Hi, You can already do FEP from one atom type to another. So particularly for combination rule 1 (see manual 5.3.2) you just choose V and W how you want. But perhaps the special case also mentioned there does what you want for the other combination rules. Mark On Fri, Nov 11, 2016 at 5:45 PM

[gmx-users] Request on initial velocities

Dear Gromacs users, I am experiencing an issue in trying to perform a dynamics run by feeding in my own starting velocities. My procedure is as in the following: 1) I build my .gro file with the desired starting position and velocities; 2) I choose the flag "no" for the "gen-vel" option in the

[gmx-users] ecomposition of Lennard-Jones contributions in free energy calculations with Gromacs

Dear gromacs users and developers, I would like to decouple independently the dispersion and repulsion components of the Lennard-Jones term in a FEP/TI run such as it happens with electrostatics and Lennard-Jones interactions. How can I do this decouple independently?. I know the great effort

Re: [gmx-users] Request on initial velocities

Hi, The vv integrators write velocities on the full step, but those in the .tpr file are interpreted as occurring on the previous half step (which is consistent with how the leap-frog integrators start up). So a half-step of integration (ie. of velocities) takes place before any trajectory output

[gmx-users] Umbrella Sampling - LINCS error when pull group is in vapor phase

Hi, I am trying to calculate the adsorption free energy of a molecule onto water. I want to use umbrella sampling to obtain the free energy profile as a function of distance normal to a water surface. I am getting LINCS error when my molecule is in the vapor phase. The error messages indicate

Re: [gmx-users] steered molecular dynamics

Hi Sir, Many thanks for the help. I would like to run steered molecular dynamics (SMD) in my protein complex system to find out the PMF without using umbrella sampling. In the tutorial: after equilibration, the steps are: (a) Generating Configurations: pull code are used, configurations files

[gmx-users] steered molecular dynamics

Hi, I would like to run steered molecular dynamics (SMD) in my protein complex system to find out the PMF without using umbrella sampling. In the tutorial:after equilibration, the steps are: (a) Generating Configurations: pull code are used, configurations files are generated, (b) umbrella